FAIR Bioinformatics

Bioinformatic talks 14/12/2022

Izar de Villasante

Motivation

Next generation notebooks
- better integration of code plots and narrative
Portable workspace
- platform independent working environment (cluster, local, remote, OS)
- Avoid involving it or admins in software installation on remote cluster (HPC)
Community feedback
- Good opportunity to share new discoveries about remote work (both remote server & homebased work)
- Good opportunity to hear about other approaches
- Discussion with the bioinformatics community.
- Inspiration for Bioinformatics Unit Workshops

:::

FAIR PRINCIPLES

Findable

Accessible

Interoperable

Reusable

Easy to find for both humans and computers. Globally unique & persistent id.

Open as possible, closed as necessary. User authentication and authorisation.

Can be integrated with other apps & analysis

Documentation and settings, clear license.

“Fair is everybody getting what they need. if you want it fair start by yourself”

So what is Quarto?

Quarto is the next-generation of RMarkdown.

For everyone.

So what is Quarto?

Quarto is a command line interface (CLI) that renders plain text formats (.qmd, .rmd, .md) OR mixed formats (.ipynb/Jupyter notebook) into static PDF/Word/HTML reports, books, websites, presentations and more

idevillasante$ quarto --help

  Usage:   quarto
  Version: 1.0.36

  Description:
    Quarto CLI

  Options:
    -h, --help     - Show this help.                            
    -V, --version  - Show the version number for this program.  

  Commands:
    render          [input] [args...]   - Render input file(s) to various document types.            
    preview         [file] [args...]    - Render and preview a document or website project.          
    serve           [input]             - Serve a Shiny interactive document.                        
    create-project  [dir]               - Create a project for rendering multiple documents          
    convert         <input>             - Convert documents to alternate representations.            
    pandoc          [args...]           - Run the version of Pandoc embedded within Quarto.          
    run             [script] [args...]  - Run a TypeScript, R, Python, or Lua script.                
    install         <type> [target]     - Installs an extension or global dependency.                
    publish         [provider] [path]   - Publish a document or project. Available providers include:
    check           [target]            - Verify correct functioning of Quarto installation.         
    help            [command]           - Show this help or the help of a sub-command.

Quarto, more than just `knitr`

Rmarkdown document processing workflow… . . .

Quarto, more than just `knitr`

Jupyter notebooks workflow…

Quarto, more than just `knitr`

Quarto notebooks combine dual engine … Knitr

Quarto, more than just `knitr`

Quarto notebooks combine dual engine … or jupyter

Quarto, more internals

knitr or jupyter evaluates R/Python/Julia code and returns a .md file along with the evaluated code

Quarto applies Lua filters + CSS/LaTeX which is then evaluated alongside the .md file by Pandoc and converted to a final ouput format

Here is an example of a Lua filter that converts strong emphasis to small caps, from https://pandoc.org/lua-filters.html

return {
  {
    Strong = function (elem)
      return pandoc.SmallCaps(elem.c)
    end,
  }
}

Lua filters written by R/Python/Julia developers should be interchangeable between formats - not language specific!

Comfort of your own workspace

A screenshot of a Quarto document rendered inside RStudio

A screenshot of a Quarto document rendered inside JupyterLab

A screenshot of a Quarto document rendered inside VSCode

So what is Quarto?

Quarto® is an open-source scientific and technical publishing system built on Pandoc

So what is Quarto?

A Quarto document i.e. a .qmd is a plain text file, like a .rmd, that can be rendered to many different formats

A screenshot of a Visual and Source Quarto document

One install, “Batteries included”

RMarkdown grew into a large ecosystem, with varying syntax.

Quarto comes “batteries included” straight out of the box

HTML reports and websites
PDF reports
MS Office (Word, Powerpoint)
Presentations (Powerpoint, Beamer, revealjs)
Books

Any language, exact same approach and syntax

What to do with my existing `.Rmd` or `.ipynb`?

For some of you - nothing changes! Keep using RMarkdown and Jupyter.

However, most existing .rmd or .ipynb can be rendered as-is via Quarto

quarto render my-favorite.rmd --to html

Since Jupyter notebooks can either be treated as a linear document to be re-executed or an already evaluated document there are additional options like: --execute

quarto render my-favorite.ipynb --to html --execute

Quarto comes out of the box with much better accessibility, better defaults, more options, and a much more consistent syntax.

Rendering

Render in RStudio

System shell via quarto render

quarto render document.qmd # defaults to html
quarto render document.qmd --to pdf
quarto render document.qmd --to docx

R console via quarto R package

library(quarto)
quarto_render("document.qmd") # defaults to html
quarto_render("document.qmd", output_format = "pdf")

Summary of Quarto > RMarkdown

Easier to organize/structure document and document layout
Features largely cross-format
Better ability to integrate multiple languages in a PROJECT
Evaluate native language (R in knitr, Python/Julia in Jupyter)
HTML slides with revealjs are pandoc-compatible, so RStudio Visual Editor works with them

ROCKER-project

+ = https://www.rocker-project.org/

The rocker project provides a collection of containers suited for different needs. find a base image to extend or images with popular software and optimized libraries pre-installed. Get the latest version or a reproducibly fixed environment.